Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020142.1 Corchorus olitorius cultivar O-4 contig20175, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2440
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35


Found at i:1024 original size:54 final size:55

Alignment explanation


    Indices: 937--1052  Score: 180
    Period size: 54  Copynumber: 2.1  Consensus size: 55

        927 TAATTATTAG

                       *                                     *      
        937 TTTCATTTCACGCAATAAATGTTATAATAAATCCTAT-CCCTATCTCTATTTAATT
          1 TTTC-TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATT

                                                                    
        992 TTTCTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATT
          1 TTTCTTTCACACAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATT

            *    
       1048 ATTCT
          1 TTTCT

       1053 ACAAAATAAA


Statistics
Matches: 56,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  54   31  0.55
  55    4  0.07
  56   21  0.38

ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43


Consensus pattern (55 bp):   
TTTCTTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATT

Found at i:1178 original size:42 final size:42

Alignment explanation


    Indices: 1119--1198  Score: 133
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       1109 AAGGATCAGG

                                      *               
       1119 ATTTGAGTTGAGTATTTCATAATTTATAAAGAATTTTCTATA
          1 ATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTCTATA

                              *         *         
       1161 ATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 ATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTC

       1199 AAGACTTAGC


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  42   35  1.00

ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47


Consensus pattern (42 bp):   
ATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTCTATA

Found at i:1183 original size:21 final size:21

Alignment explanation


    Indices: 1119--1185  Score: 66
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1109 AAGGATCAGG

                              *  
       1119 ATTTGAGTTGAGTATTTCATA
          1 ATTTGAGTTGAGTATTTCTTA

                    **  *          
       1140 ATTT-A-TAAAGAATTTTCTATA
          1 ATTTGAGTTGAGTA-TTTCT-TA

                                 
       1161 ATTTGAGTTGAGTATTTCTTA
          1 ATTTGAGTTGAGTATTTCTTA

                
       1182 ATTT
          1 ATTT

       1186 ACAGAGAATT


Statistics
Matches: 35,  Mismatches: 7, Indels: 8
        0.70            0.14        0.16

Matches are distributed among these distances:
  19    4  0.11
  20    5  0.14
  21   16  0.46
  22    6  0.17
  23    4  0.11

ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51


Consensus pattern (21 bp):   
ATTTGAGTTGAGTATTTCTTA
Done.